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Use ImageJ from Python
https://pyimagej.readthedocs.io/
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Cannot initialize pyimagej inside windows (conda) #121

Closed ghost closed 3 years ago

ghost commented 3 years ago

I have tried this for several months and still no progress. Always getting errors when initializing pyimagej. Please help this Windows guinea pig. Does this seem to be related to proxy settings? Sorry for my naive questions.

I'm using Windows 10 64 bit.

conda create -n test_imagej pyimagej openjdk=8 conda activate pyimagej python

then

Python 3.6.13 (default, Feb 19 2021, 05:17:09) [MSC v.1916 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

import imagej ij = imagej.init(['net.imagej:imagej:2.0.0-rc-71', 'net.imagej:imagej-legacy:0.37.4']) Error in `C:\Users\Z036650\Anaconda3\envs\test_pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-legacy-0.37.4+net.imagej-imagej-2.0.0-rc-71\pom.xml dependency:resolve': 1

ij = imagej.init(['net.imagej:imagej', 'net.imagej:imagej-legacy']) Error in `C:\Users\Z036650\Anaconda3\envs\test_pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-RELEASE+net.imagej-imagej-legacy-RELEASE\pom.xml dependency:resolve': 1

ij = imagej.init() Error in `C:\Users\Z036650\Anaconda3\envs\test_pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-RELEASE+net.imagej-imagej-legacy-RELEASE\pom.xml dependency:resolve': 1

ij = imagej.init(['net.imagej:imagej:2.1.0', 'net.imagej:imagej-legacy']) Error in `C:\Users\Z036650\Anaconda3\envs\test_pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-legacy-RELEASE+net.imagej-imagej-2.1.0\pom.xml dependency:resolve': 1

ij = imagej.init('D:\Fiji.app') Error in `C:\Users\Z036650\Anaconda3\envs\test_pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\1.0.0\pom.xml dependency:resolve': 1

My environment (test_pyimagej) PS C:\Users\Z036650> conda list # packages in environment at C:\Users\Z036650\Anaconda3\envs\test_pyimagej: #

Name Version Build Channel

certifi 2021.5.30 py36ha15d459_0 conda-forge cycler 0.10.0 py_2 conda-forge freetype 2.10.4 h546665d_1 conda-forge imglyb 1.0.0 pyh050c7b8_0 conda-forge intel-openmp 2021.2.0 h57928b3_616 conda-forge jbig 2.1 h8d14728_2003 conda-forge jgo 1.0.0 pyhd8ed1ab_0 conda-forge jpeg 9d h8ffe710_0 conda-forge jpype1 1.2.1 py36he95197e_0 conda-forge kiwisolver 1.3.1 py36he95197e_1 conda-forge lcms2 2.12 h2a16943_0 conda-forge lerc 2.2.1 h0e60522_0 conda-forge libblas 3.9.0 9_mkl conda-forge libcblas 3.9.0 9_mkl conda-forge libdeflate 1.7 h8ffe710_5 conda-forge liblapack 3.9.0 9_mkl conda-forge libpng 1.6.37 h1d00b33_2 conda-forge libtiff 4.3.0 h0c97f57_1 conda-forge lz4-c 1.9.3 h8ffe710_0 conda-forge matplotlib-base 3.3.4 py36h1abdf75_0 conda-forge maven 3.6.3 h57928b3_0 conda-forge mkl 2021.2.0 hb70f87d_389 conda-forge numpy 1.19.5 py36hd1b969e_1 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjdk 8.0.282 h57928b3_0 conda-forge openjpeg 2.4.0 hb211442_1 conda-forge pandas 0.25.3 py36he350917_0 conda-forge pillow 8.2.0 py36h9cbe6be_1 conda-forge pip 21.1.2 pyhd8ed1ab_0 conda-forge psutil 5.8.0 py36h68aa20f_1 conda-forge pyimagej 1.0.0 py36ha15d459_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge python 3.6.13 h39d44d4_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge scyjava 1.1.0 pyhd8ed1ab_0 conda-forge setuptools 49.6.0 py36ha15d459_3 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge tbb 2021.2.0 h2d74725_0 conda-forge tk 8.6.10 h8ffe710_1 conda-forge tornado 6.1 py36h68aa20f_1 conda-forge typing_extensions 3.10.0.0 pyha770c72_0 conda-forge vc 14.2 hb210afc_4 conda-forge vs2015_runtime 14.28.29325 h5e1d092_4 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge wincertstore 0.2 py36ha15d459_1006 conda-forge xarray 0.18.2 pyhd8ed1ab_0 conda-forge xz 5.2.5 h62dcd97_1 conda-forge zlib 1.2.11 h62dcd97_1010 conda-forge zstd 1.5.0 h6255e5f_0 conda-forge

hinerm commented 3 years ago

@phamtronglam

ij = imagej.init('D:\Fiji.app')

It looks like there is a bug where if you try to initialize pyimagej with a local app after failing to do so with a Maven endpoint, it doesn't work. You have to restart your interpreter. Also I believe you need to escape the backslash:

ij = imagej.init('D:\\Fiji.app')

As for the other error messages, to try and better understand what's going on can you: 1 . Remove your ~/.jgo folder before trying initialization again

  1. Add these lines to the top of your script: 
    import logging
logging.basicConfig(level = logging.DEBUG)

That should result in more information being printed out.

Thank you!

ghost commented 3 years ago

@hinerm
Thank you very much for your support. I have tried as you told, but no success.

  1. Remove ~.jgo
  2. Create new environment from beginning for testing (should be the same with previous situation) conda create -n pyimagej pyimagej openjdk=8
  3. Run (with proper debug and escape path character) import logging logging.basicConfig(level = logging.DEBUG) import imagej ij = imagej.init('D:\\fiji-win64\\Fiji.app')

Errors are as follows. Please help me check. It seems that the JAR plugins are loaded successfully. However some download later failed? I'm sorry I'm not familiar with Maven or Java.

I'm behind a firewall in company. I even tried to set HTTP_PROXY and HTTPS_PROXY in the beginning of C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.cmd, but the output errors are still the same.

is there a way to manually (or in python scripts) download these dependencies from maven.scijava before running ij = imagtj.init("local FIJI")?

Thank you very much.

`(pyimagej) PS D:\tmp> (pyimagej) PS D:\tmp> python Python 3.6.13 (default, Sep 23 2021, 07:38:49) [MSC v.1916 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

import logging logging.basicConfig(level = logging.DEBUG) import imagej DEBUG:matplotlib:CONFIGDIR=C:\Users\Z036650.matplotlib DEBUG:matplotlib:(private) matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data DEBUG:matplotlib:matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data DEBUG:matplotlib:loaded rc file C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data\matplotlibrc DEBUG:matplotlib:matplotlib version 3.2.2 DEBUG:matplotlib:interactive is False DEBUG:matplotlib:platform is win32 DEBUG:matplotlib:loaded modules: ['builtins', 'sys', '_frozen_importlib', '_imp', '_warnings', '_thread', '_weakref', '_frozen_importlib_external', '_io', 'marshal', 'nt', 'winreg', 'zipimport', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', 'main', 'encodings.latin_1', 'io', 'abc', '_weakrefset', 'site', 'os', 'errno', 'stat', '_stat', 'ntpath', 'genericpath', 'os.path', '_collections_abc', '_sitebuiltins', 'sysconfig', '_bootlocale', '_locale', 'encodings.cp932', '_codecs_jp', '_multibytecodec', 'types', 'functools', '_functools', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'weakref', 'collections.abc', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'mpl_toolkits', 'atexit', 'logging', 'time', 'traceback', 'linecache', 'tokenize', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 'copyreg', 'token', 'string', '_string', 'threading', 'imagej', 'imglyb', 'scyjava', 'jgo', 'jgo.jgo', 'argparse', 'copy', 'textwrap', 'gettext', 'locale', 'struct', '_struct', 'configparser', 'glob', 'fnmatch', 'posixpath', 'pathlib', 'urllib', 'urllib.parse', 'shutil', 'zlib', 'bz2', '_compression', '_bz2', 'lzma', '_lzma', 'subprocess', 'signal', 'msvcrt', 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'_csv', 'gzip', 'http', 'http.client', 'email.message', 'uu', 'email._encoded_words', 'email.iterators', 'ssl', 'ipaddress', '_ssl', 'mmap', 'urllib.error', 'urllib.response', 'urllib.request', 'nturl2path', 'pandas.core.internals.construction', 'pandas.core.series', 'pandas._libs.reshape', 'pandas.core.indexes.accessors', 'pandas.plotting', 'pandas.plotting._core', 'pandas.plotting._matplotlib', 'pandas.plotting._matplotlib.boxplot', 'matplotlib', 'matplotlib.cbook', 'shlex', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.fontconfig_pattern', 'pyparsing', 'pyparsing.util', 'pyparsing.exceptions', 'pyparsing.unicode', 'pyparsing.actions', 'pyparsing.core', 'pyparsing.results', 'pyparsing.helpers', 'html', 'html.entities', 'pyparsing.testing', 'pyparsing.common', 'matplotlib.colors', 'matplotlib.docstring', 'matplotlib._color_data', 'cycler', 'matplotlib._version', 'matplotlib.ft2font', 'kiwisolver'] DEBUG:matplotlib:CACHEDIR=C:\Users\Z036650.matplotlib DEBUG:matplotlib.font_manager:Using fontManager instance from C:\Users\Z036650.matplotlib\fontlist-v310.json ij = imagej.init("D:\fiji-win64\Fiji.app") DEBUG:imagej:Local path to ImageJ installation given: D:\fiji-win64\Fiji.app DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ahocorasick-0.2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/alphanumeric-comparator-1.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/annotations-13.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ant-1.9.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ant-launcher-1.9.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/antlr-3.5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/antlr-runtime-3.5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/api-common-1.9.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/args4j-2.0.25.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/artoolkitplus-2.3.1-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/asm-7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/asm-analysis-7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/asm-commons-7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/asm-tree-7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/asm-util-7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/auto-value-annotations-1.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/autocomplete-3.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/aws-java-sdk-core-1.11.796.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/aws-java-sdk-kms-1.11.796.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/aws-java-sdk-s3-1.11.796.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/base64-2.3.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batch-processor-0.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-anim-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-awt-util-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-bridge-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-codec-1.10.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-constants-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-css-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-dom-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-ext-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-gvt-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-i18n-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-parser-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-script-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-shared-resources-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-svg-dom-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-svggen-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-transcoder-1.10.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-util-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/batik-xml-1.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bcpkix-jdk15on-1.62.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bcprov-jdk15on-1.62.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-bioformats-0.2.15.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-core-10.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-playground-0.3.8-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-selector-0.1.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-spimdata-extras-0.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigdataviewer-vistools-1.0.0-beta-28.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bigvolumeviewer-0.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bij-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/blas-0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bounce-0.18.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bsh-2.0b6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/bytelist-1.0.15.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/byteunits-0.9.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/c3p0-0.9.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/caffeine-2.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/cdm-4.6.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/clojure-1.8.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/codemodel-2.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/collections-generic-4.01.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/common-image-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/common-io-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/common-lang-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-beanutils-1.9.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-codec-1.14.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-collections-3.2.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-collections4-4.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-compress-1.18.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-io-2.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-lang-2.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-lang3-3.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-logging-1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-math-2.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-math3-3.6.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-net-3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-pool2-2.8.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-text-1.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/commons-vfs2-2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/Compiler.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/cuda-9.0-7.0-1.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/datasets-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/datavec-api-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/datavec-data-image-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-common-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-core-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-datasets-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-datavec-iterators-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-modelimport-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-nn-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-tsne-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-ui-components-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/deeplearning4j-utility-iterators-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/dirgra-0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ejml-0.24.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/error_prone_annotations-2.3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/eventbus-1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/f2jutil-0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/failureaccess-1.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/FastInfoset-1.2.16.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/fastutil-6.5.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ffmpeg-4.2.2-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ffmpeg-platform-4.1-1.4.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/fiji-2.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/fiji-compat-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/fiji-lib-2.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/filters-2.0.235.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/flandmark-1.07-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/flatbuffers-java-1.10.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/flycapture-2.13.3.31-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/fontchooser-2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/freemarker-2.3.23.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gax-1.56.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gax-httpjson-0.73.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gcc-runtime-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gentyref-1.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gluegen-rt-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gluegen-rt-main-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-api-client-1.30.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-api-services-cloudresourcemanager-v1-rev20200210-1.30.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-api-services-storage-v1-rev20200326-1.30.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-auth-library-credentials-0.20.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-auth-library-oauth2-http-0.20.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-cloud-core-1.93.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-cloud-core-http-1.93.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-cloud-resourcemanager-0.117.2-alpha.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-cloud-storage-1.108.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-http-client-1.40.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-http-client-appengine-1.40.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-http-client-jackson2-1.40.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-http-client-xml-1.40.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/google-oauth-client-1.30.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gpars-1.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gpcj-2.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/graphics-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/grDevices-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-dateutil-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-json-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-swing-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-templates-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/groovy-xml-3.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/grpc-context-1.22.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/gson-2.8.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/guava-21.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-1.12.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/hdf5-platform-1.12.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/httpclient-4.5.12.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/httpcore-4.4.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/httpmime-4.5.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/httpservices-4.6.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/icu4j-59.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ij-1.53f.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ij1-patcher-1.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ij_blob-1.4.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/image4j-0.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-bmp-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-core-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-jpeg-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-metadata-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-psd-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imageio-tiff-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-2.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-common-0.34.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-deprecated-0.1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-launcher-6.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-legacy-0.38.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-mesh-0.8.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-mesh-io-0.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-notebook-0.7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-ops-0.45.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-plugins-batch-0.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-plugins-commands-0.8.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-plugins-tools-0.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-plugins-uploader-ssh-0.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-plugins-uploader-webdav-0.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-scripting-0.8.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-ui-awt-0.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-ui-swing-0.23.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-updater-0.10.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imagej-utils-0.6.4-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-5.12.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-algorithm-0.12.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-algorithm-fft-0.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-algorithm-gpl-0.2.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-cache-1.0.0-beta-16.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-ij-2.0.0-beta-46.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-label-multisets-0.10.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-labkit-0.2.10.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-realtransform-3.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-roi-0.11.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-trainable-segmentation-0.1.11.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/imglib2-ui-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/invokebinder-1.10.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ion-java-1.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/istack-commons-runtime-3.0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/itextpdf-5.5.13.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ivy-2.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/j2objc-annotations-1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/j3dcore-1.6.0-scijava-2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/j3dutils-1.6.0-scijava-2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackrabbit-webdav-2.21.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-annotations-2.12.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-core-2.12.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-databind-2.12.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-dataformat-cbor-2.12.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jackson-jq-1.0.0-preview.20191208.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jai-codec-1.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jai-core-1.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jai-imageio-core-1.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jakarta.activation-api-1.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jakarta.xml.bind-api-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jama-1.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/java-cup-11b-20160615.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/java-sizeof-0.0.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javabuilder-9.2.0.538062.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-android-arm.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-android-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-android-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-ios-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacpp-platform-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javacv-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javaGeom-0.11.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javassist-3.27.0-GA.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javax.annotation-api-1.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javax.json-1.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/javax.servlet-api-3.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jaxb-runtime-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jblosc-1.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jclipboardhelper-0.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jcodings-1.0.55.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jcommander-1.48.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jcommon-1.0.24.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jdatepicker-1.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jdom2-2.0.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jep-2.4.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jffi-1.2.19-native.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jffi-1.2.20.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jfilechooser-bookmarks-0.1.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jfreechart-1.5.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jfreesvg-3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jgoodies-common-1.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jgoodies-forms-1.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jgrapht-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jgrapht-core-1.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jgraphx-4.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jhdf5-14.12.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jheaps-0.11.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jhotdraw-7.6.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jitk-tps-3.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jline-2.14.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jmespath-java-1.11.796.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jna-4.5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jna-platform-4.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-a64asm-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-constants-0.9.12.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-enxio-0.16.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-ffi-2.1.10.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-netdb-1.1.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-posix-3.0.50.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-unixsocket-0.17.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jnr-x86asm-1.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/joal-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/joal-main-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jocl-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jocl-main-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/joda-time-2.10.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jogl-all-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jogl-all-main-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/joml-1.9.25.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/joni-2.1.29.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jpedalSTD-2.80b11.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jply-0.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jruby-core-9.1.17.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jruby-stdlib-9.1.17.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jsch-0.1.55.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/json-20090211.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jsoup-1.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jsr166y-1.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jsr305-3.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jtransforms-2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jung-api-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jung-graph-impl-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/JWlz-1.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jython-shaded-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jython-slim-2.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/jzlib-1.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/Kappa-2.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/kotlin-stdlib-1.4.21.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/kotlin-stdlib-common-1.4.21.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/kryo-4.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/languagesupport-3.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/lapack-0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/legacy-imglib1-1.1.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-android-arm.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-android-arm64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-android-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-android-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-1.79.0-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/leptonica-platform-1.79.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/libdc1394-2.2.6-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/libfreenect-0.5.7-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/libfreenect2-0.2.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/librealsense-1.12.4-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/librealsense2-2.29.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/log4j-1.2.17.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/log4j-over-slf4j-1.7.27.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/logback-classic-1.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/logback-core-1.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/lz4-java-1.7.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mapdb-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/markdownj-0.3.0-1.0.2b4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mastodon-1.0.0-beta-17.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/maven-scm-api-1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/maven-scm-provider-svn-commons-1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/maven-scm-provider-svnexe-1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mchange-commons-java-0.2.15.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/metadata-extractor-2.11.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/methods-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/miglayout-core-5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/miglayout-swing-5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mines-jtk-20151125.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/minimaven-2.2.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/minio-5.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/minlog-1.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-2020.1-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mkl-platform-2020.1-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/modulator-1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mpicbg-1.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/mtj-1.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/multiverse-core-0.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-2.5.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-aws-s3-3.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-blosc-1.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-google-cloud-3.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-hdf5-1.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-ij-3.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-imglib2-4.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/n5-zarr-0.0.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nailgun-server-0.9.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/native-lib-loader-2.3.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-api-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-common-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-guava-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-android-arm.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-android-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-android-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-api-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nd4j-native-platform-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/nearestneighbor-core-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/neoitertools-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netcdf-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-buffer-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-codec-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-common-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-handler-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-resolver-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/netty-transport-4.1.45.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/object-inspector-0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/objenesis-2.5.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ojalgo-45.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/okhttp-4.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/okio-2.6.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/OMEVisual-2.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/op-finder-0.1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-android-arm.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-android-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-android-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-ios-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-0.3.9-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/openblas-platform-0.3.9-1-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencensus-api-0.24.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencensus-contrib-http-util-0.24.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencsv-5.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-android-arm.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-android-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-android-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-ios-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-linux-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-linux-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-macosx-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-windows-x86.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-4.3.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/opencv-platform-4.3.0-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/options-1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/oshi-core-3.4.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/oshi-json-3.4.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/oswego-concurrent-1.3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/pal-optimization-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/parsington-2.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/perf4j-0.9.16.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/plexus-utils-1.5.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/postgresql-42.2.12.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/prettytime-4.0.1.Final.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/proto-google-common-protos-1.17.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/proto-google-iam-v1-0.13.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/protobuf-1.0.0-beta7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/protobuf-java-3.11.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/protobuf-java-util-3.11.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/reflectasm-1.11.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/regexp-1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/REngine.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/renjin-appl-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/renjin-core-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/renjin-gnur-runtime-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/renjin-script-engine-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/rhino-1.7.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/RserveEngine.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/rsyntaxtextarea-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/runAC-1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scala-compiler-2.12.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scala-library-2.12.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scala-reflect-2.12.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scala-xml_2.12-1.0.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-0.42.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-bf-compat-4.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-cli-0.6.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-hdf5-0.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-jai-imageio-1.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-lifesci-0.9.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scifio-ome-xml-0.16.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-common-2.87.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-config-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-io-http-0.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-listeners-1.0.0-beta-3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-optional-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-plugins-commands-0.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-plugins-io-table-0.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-plugins-platforms-0.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-plugins-text-markdown-0.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-plugins-text-plain-0.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-search-0.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-table-0.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-ui-awt-0.1.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scijava-ui-swing-0.13.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/script-editor-0.5.9.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-beanshell-0.3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-clojure-0.1.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-groovy-0.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-java-0.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-javascript-0.5.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-jruby-0.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-jython-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-renjin-0.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/scripting-scala-0.2.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/segmentation-annotator-0.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/serializer-2.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/slf4j-api-1.7.27.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/slf4j-nop-1.7.27.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/snakeyaml-1.26.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/spim_data-2.2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/sqlite-jdbc-3.28.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ST4-4.0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/stats-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/stax-ex-1.8.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/stream-2.9.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/swing-checkbox-tree-1.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/swing-worker-1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/swingx-1.6.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/t-digest-3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/T2-NIT-1.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/T2-TreelineGraph-1.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/tesseract-4.1.1-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/threetenbp-1.3.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/TrackMate-7.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/trakem2-transform-1.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/trove4j-3.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/txw2-2.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/udunits-4.3.18.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ui-behaviour-2.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/unsafe-fences-1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/utils-0.8.1906.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/vecmath-1.6.0-scijava-2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/VectorGraphics2D-0.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/VectorString-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/VIB-lib-2.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/videoinput-0.200-1.5.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/weave_jy2java-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/weka-dev-3.9.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xalan-2.7.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xchart-3.5.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xerbla-0.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xercesImpl-2.8.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xml-apis-ext-1.3.04.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xmlgraphics-commons-2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xmpcore-5.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xpp3-1.1.4c.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/xz-1.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/yecht-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/formats-api-6.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/formats-bsd-6.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/formats-gpl-6.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/jai_imageio-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/jxrlib-all-0.2.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/metakit-5.3.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-codecs-0.3.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-common-6.0.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-jai-0.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-mdbtools-5.3.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-poi-5.3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/ome-xml-6.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/specification-6.2.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\bio-formats/turbojpeg-6.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/ffmpeg-4.1-1.4.4-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/gluegen-rt-2.3.2-natives-windows-amd64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/joal-2.3.2-natives-windows-amd64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/jocl-2.3.2-natives-windows-amd64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/jogl-all-2.3.2-natives-windows-amd64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars\win64/opencv-windows-x86_64.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/3D_Blob_Segmentation-3.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/3D_Objects_Counter-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/3DViewer-4.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/AnalyzeSkeleton-3.4.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Anisotropic_Diffusion_2D-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/annotator_Project-0.0.3-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ArchipelagoPlugins-0.5.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Arrow-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Auto_Local_Threshold-1.10.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/AutoThreshold-1.17.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/BalloonSegmentation-3.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/bigdataviewer_fiji-6.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/bigwarp_fiji-7.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/bio-formats_plugins-6.7.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/BiovoxxelPlugins-2.5.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/blockmatching-2.1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/BugSubmitter-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/bUnwarpJ-2.6.13.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Calculator_Plus-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Cell_Counter-3.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Colocalisation_Analysis-3.0.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Color_Histogram-2.0.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Color_Inspector_3D-2.5.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ColourDeconvolution-3.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/CorrectBleach-2.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Correct_3D_Drift-1.0.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/CPUMeter-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/DeepImageJ-1.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Descriptor_basedregistration-2.1.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Dichromacy-2.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Directionality_-2.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Feature_Detection-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Fiji_Archipelago-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Fiji_Developer-2.0.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Fiji_Package_Maker-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/FijiPlugins-3.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/FlowJ-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/FS_Align_TrakEM2-2.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Gran_Filter.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Graph_Cut-1.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Gray_Morphology-2.3.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/H5J_Loader_Plugin-1.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/HDF5_Vibez-1.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Helmholtz_Analysis-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Hough_Circle_Transform-1.0.0-RELEASE.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_ellipse_split-0.4.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_irregular_watershed-1.0.0-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_nanotrackj-1.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_ndef_ext-1.2.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_nl_means-1.4.7.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_ridge_detect-1.4.1-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/IJ_Robot-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_r_plot-0.6-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_shape_filter-1.4.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ij_shape_smoothing-1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ilastik4ij-1.8.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Image_5D-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/image_edge.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Image_Expression_Parser-3.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Interactive_3D_SurfacePlot-3.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/IO-4.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/IsoData_Classifier-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Jay_Plugins (1).jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Kuwahara_Filter-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/KymographBuilder-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Lasso_and_Blow_Tool-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/level_sets-1.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/libtensorflow_jni_gpu-1.15.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/LinearKuwahara-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/LocalThickness-4.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/LSM_Reader-4.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/LSM_Toolbox-4.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ManualTracking-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/MorphoLibJ-1.4.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/mpicbg-1.4.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/MTrack2-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Multi_Kymograph-3.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/M_I_P-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/n5-viewerfiji-4.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/panorama-3.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ParticleSizer_-1.0.9-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/PIVanalyser-1.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/QuickPALM-1.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/QuiverPlot-0.2.0-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/RATS-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Reconstruct_Reader-2.0.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/register_virtual_stack_slices-3.0.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/registration3d-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Samples-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SCF_ImgTools-1.3.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Series_Labeler-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Sholl_Analysis-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Simple_Neurite_Tracer-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SioxSegmentation-1.0.5.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Skeletonize3D-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SPIM_Opener-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SPIMRegistration-5.0.22.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SplineDeformationGenerator-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/SpotColocalizer-1.0.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Stack_Manipulation-2.1.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Statistical_RegionMerging-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Stitching-3.1.8.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Sync_Win-1.7-fiji4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Thread_Killer-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Time_Lapse-2.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TimeStamper-2.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/ToAST-25.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TopoJ-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TrackMate-0.0.0-STUB.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TrainableSegmentation-3.3.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TrakEM2-1.3.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/TrakEM2_Archipelago-2.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/trakem2_tps-1.1.4.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Vaa3d_Reader-2.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Vaa3dWriter-1.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/VIB-3.0.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/VideoEditing-2.0.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/View5D-2.3.6.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Volume_Calculator-2.0.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/Volume_Viewer-2.01.2.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins/zspacing-1.1.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/Compiler.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/hamcrest-core-1.3.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/junit-4.12.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/libtensorflow-1.15.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/proto-1.12.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\jars/protobuf-java-3.2.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\OrientationJ/OrientationJ.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\SCF-MPICBG/InteractiveWatershed-1.2.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig/ScientiFig_-3.1-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig/ScientiFig_external_launcher-1.0-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Icons-1.0-SNAPSHOT.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/REngine-2.1.0-sources.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/REngine-2.1.0.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Rserve-1.8.1-sources.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Rserve-1.8.1.jar DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\Skeleton Analysis/Skeleton_Intersections.jar INFO:imagej:Added 679 JARs to the Java classpath. DEBUG:scyjava:Adding jars from endpoints ['net.imglib2:imglib2-imglyb:1.0.1'] DEBUG:scyjava:Using endpoints ['net.imglib2:imglib2-imglyb:1.0.1'] DEBUG:scyjava.config:Getting verbose level: 0 DEBUG:jgo:Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1. INFO:jgo:First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions. DEBUG:jgo:Executing: ('C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.CMD', '-B', '-f', 'C:\Users\Z036650\.jgo\net.imglib2\imglib2-imglyb\f4fac80b03fce85723c2b54c1deacf30529c353c36bdd7faa51bddb191df9081\pom.xml', 'dependency:resolve') ERROR:jgo:Error in `C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.CMD -B -f C:\Users\Z036650.jgo\net.imglib2\imglib2-imglyb\f4fac80b03fce85723c2b54c1deacf30529c353c36bdd7faa51bddb191df9081\pom.xml dependency:resolve': 1 DEBUG:jgo:Exception: Command '('C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.CMD', '-B', '-f', 'C:\Users\Z036650\.jgo\net.imglib2\imglib2-imglyb\f4fac80b03fce85723c2b54c1deacf30529c353c36bdd7faa51bddb191df9081\pom.xml', 'dependency:resolve')' returned non-zero exit status 1. DEBUG:jgo:Debug Trace: Traceback (most recent call last): File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\jgo\jgo.py", line 274, in run_and_combine_outputs return subprocess.check_output(command_string, stderr=subprocess.STDOUT) File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\subprocess.py", line 356, in check_output **kwargs).stdout File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\subprocess.py", line 438, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '('C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.CMD', '-B', '-f', 'C:\Users\Z036650\.jgo\net.imglib2\imglib2-imglyb\f4fac80b03fce85723c2b54c1deacf30529c353c36bdd7faa51bddb191df9081\pom.xml', 'dependency:resolve')' returned non-zero exit status 1. DEBUG:jgo: std out: DEBUG:jgo: [INFO] Scanning for projects...\r DEBUG:jgo: [INFO] Downloading from scijava.public: https://maven.scijava.org/content/groups/public/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom\r DEBUG:jgo: [INFO] Downloading from central: https://repo.maven.apache.org/maven2/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom\r DEBUG:jgo: [ERROR] [ERROR] Some problems were encountered while processing the POMs:\r DEBUG:jgo: [ERROR] Non-resolvable import POM: Could not transfer artifact net.imglib2:imglib2-imglyb:pom:1.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): Transfer failed for https://maven.scijava.org/content/groups/public/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom @ line 8, column 29\r DEBUG:jgo: @ \r DEBUG:jgo: [ERROR] The build could not read 1 project -> [Help 1]\r DEBUG:jgo: [ERROR] \r DEBUG:jgo: [ERROR] The project net.imglib2-BOOTSTRAPPER:imglib2-imglyb-BOOTSTRAPPER:0 (C:\Users\Z036650\.jgo\ DEBUG:jgo: et.imglib2\imglib2-imglyb\f4fac80b03fce85723c2b54c1deacf30529c353c36bdd7faa51bddb191df9081\pom.xml) has 1 error\r DEBUG:jgo: [ERROR] Non-resolvable import POM: Could not transfer artifact net.imglib2:imglib2-imglyb:pom:1.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): Transfer failed for https://maven.scijava.org/content/groups/public/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom @ line 8, column 29: Connect to maven.scijava.org:443 [maven.scijava.org/144.92.48.199] failed: Connection timed out: connect -> [Help 2]\r DEBUG:jgo: [ERROR] \r DEBUG:jgo: [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.\r DEBUG:jgo: [ERROR] Re-run Maven using the -X switch to enable full debug logging.\r DEBUG:jgo: [ERROR] \r DEBUG:jgo: [ERROR] For more information about the errors and possible solutions, please read the following articles:\r DEBUG:jgo: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException\r DEBUG:jgo: [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException\r DEBUG:jgo: ' (pyimagej) PS D:\tmp>```

ctrueden commented 3 years ago

@phamtronglam Thanks very much for the debugging output!

This part is definitely a problem:

Transfer failed for https://maven.scijava.org/content/groups/public/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom Connect to maven.scijava.org:443 [maven.scijava.org/144.92.48.199] failed: Connection timed out: connect

If you click that link in your web browser from the same computer, does it load the data? Or do you get a timeout from the web browser as well? Is it possible you are behind a firewall that restricts your access to maven.scijava.org?

imagejan commented 3 years ago

@phamtronglam wrote:

I'm behind a firewall in company. I even tried to set HTTP_PROXY and HTTPS_PROXY in the beginning of C:\Users\Z036650\Anaconda3\envs\pyimagej\Library\bin\mvn.cmd, but the output errors are still the same.

@phamtronglam can you try whether adding the following block (adapted to your proxy) inside the <settings> ... </settings> section of your $HOME\.m2\settings.xml would fix the issue?

  <proxies>
    <proxy>
      <id>Your company proxy</id>
      <active>true</active>
      <protocol>https</protocol>
      <host>proxy.mycompany.com</host>
      <port>8080</port>
    </proxy>
  </proxies>

If that works for you, we can maybe find an alternative way to configure the proxy settings before running maven from jgo/pyimagej as well, to make life easier for people behind firewalls.

@ctrueden @elevans I wonder why pyimagej would still look for maven artifacts online, despite being initialized with a local path. Is that intentional?

ctrueden commented 3 years ago

I wonder why pyimagej would still look for maven artifacts online, despite being initialized with a local path. Is that intentional?

Yes, if you scrutinize the error output above carefully, you can see that endpoint it's trying to construct is net.imglib2:imglib2-imglyb:1.0.1. In other words: the needed Java-side part of imglyb. Right now, the net.imagej:imagej artifact does not include this as a dependency, nor does sc.fiji:fiji, and we don't ship it on the core update sites... so we need to mix it in ourselves, which means downloading it on demand. See also scijava/scyjava#23 for related (but not exactly this issue) discussion.

ghost commented 3 years ago

@ctrueden Thank you for your suggestion. I could access https://maven.scijava.org/content/groups/public/net/imglib2/imglib2-imglyb/1.0.1/imglib2-imglyb-1.0.1.pom normally by browser. Fortunately this is resolved as shown below.

@imagejan Thanks for the proxy setting instruction. I followed and it seems the code could go past that part. However another error related to JVM appeared. (I could also reproduce this error on another Windows machine (with same conda environment setup) without firewall restriction).

Please help me check. Side question: I could not see ~/.jgo anymore. Is it supposed behaviour (deleted temp files)? Thank you very much.


DEBUG:imagej:Local path to ImageJ installation given: D:\fiji-win64\Fiji.app
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ahocorasick-0.2.4.jar
-- This part is duplicated and not relevant to the errors anymore. So I deleted to save space.
--
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/REngine-2.1.0.jar
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Rserve-1.8.1-sources.jar
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Rserve-1.8.1.jar
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\Skeleton Analysis/Skeleton_Intersections.jar
INFO:imagej:Added 679 JARs to the Java classpath.
DEBUG:scyjava:Adding jars from endpoints []
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\imagej\__init__.py", line 165, in init
    sj.start_jvm()
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\scyjava\__init__.py", line 84, in start_jvm
    callback()
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\imglyb\util.py", line 27, in _java_setup
    Helpers                            = scyjava.jimport('net.imglib2.python.Helpers')
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\scyjava\__init__.py", line 168, in jimport
    return jpype.JClass(class_name)
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\jpype\_jclass.py", line 99, in __new__
    return _jpype._getClass(jc)
TypeError: Class net.imglib2.python.Helpers is not found``
ctrueden commented 3 years ago

@phamtronglam You are really seeing all that, including many "The JVM is already running" messages, just from the following script in a fresh Python instance?

import logging
logging.basicConfig(level = logging.DEBUG)
import imagej
ij = imagej.init('D:\\fiji-win64\\Fiji.app')

Or are you running imagej.init more than once in the same Python interpreter?

Side question: I could not see ~/.jgo anymore. Is it supposed behaviour (deleted temp files)?

If you are able to get an imagej.init(...) initialization working, you can then do:

import scyjava
print(scyjava.get_classpath())

to see the full path to each JAR file, which will show you where your jgo cache is.

You can also override where jgo puts your cache by creating a file ~/.jgorc with contents:

[settings]
cacheDir = /path/to/.jgo

TypeError: Class net.imglib2.python.Helpers is not found

That means the imglib2-imglyb library was not mixed into the environment successfully, which implies that jgo failed to construct your environment. As a workaround for now, you could try downloading it manually and dropping it into your D:\fiji-win64\Fiji.app\jars folder. Then you'd have it locally.

ghost commented 3 years ago

@ctrueden Thank you.

  1. Yes I received all that from a fresh first import logging ... imagej.init() .... [Fresh Python interpreter after fresh Windows sign out to make sure]
  2. Thank you for additional information on ~/.jgo. Unfortunately imagej.init(..) is not up yet.
  3. I tried downloading the imglib2-imglyb manually and put it under the path as you suggested. imagej.init(...) still failed. Please check. Thank you very much.
(pyimagej) PS D:\tmp> python
Python 3.6.13 (default, Sep 23 2021, 07:38:49) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import logging
>>> logging.basicConfig(level = logging.DEBUG)
>>> import imagej
DEBUG:matplotlib:CONFIGDIR=C:\Users\Z036650\.matplotlib
DEBUG:matplotlib:(private) matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data
DEBUG:matplotlib:matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data
DEBUG:matplotlib:loaded rc file C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data\matplotlibrc
DEBUG:matplotlib:matplotlib version 3.2.2
DEBUG:matplotlib:interactive is False
DEBUG:matplotlib:platform is win32
DEBUG:matplotlib:loaded modules: ['builtins', 'sys', '_frozen_importlib', '_imp', '_warnings', '_thread', '_weakref', '_frozen_importlib_external', '_io', 'marshal', 'nt', 'winreg', 'zipimport', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 
------------------------------------------
-- This should be irrelevant, so I shortened output ----
-----------------------------------------------------------
'matplotlib._color_data', 'cycler', 'matplotlib._version', 'matplotlib.ft2font', 'kiwisolver']
DEBUG:matplotlib:CACHEDIR=C:\Users\Z036650\.matplotlib
DEBUG:matplotlib.font_manager:Using fontManager instance from C:\Users\Z036650\.matplotlib\fontlist-v310.json
>>> ij = imagej.init('D:\\fiji-win64\\Fiji.app')
DEBUG:imagej:Local path to ImageJ installation given: D:\fiji-win64\Fiji.app
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/jars/ahocorasick-0.2.4.jar
----------------------------------------------------------
----------------- Similarly, this is shortened. This should be identical to the previous outputs I quoted in this issue -------------------
-----------------------------------------------------------
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\ScientiFig\lib/Rserve-1.8.1.jar
DEBUG:imagej:Added D:\fiji-win64\Fiji.app/plugins\Skeleton Analysis/Skeleton_Intersections.jar
INFO:imagej:Added 680 JARs to the Java classpath.
DEBUG:scyjava:Adding jars from endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava:Using endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava.config:Getting verbose level: 0
DEBUG:jgo:Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
----------------------------------------
-------- Tens or even a hundred of the same message. Shortened -------
--------------------------------------------
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
Traceback (most recent call last):
  File "ClassLoader.java", line 522, in java.lang.ClassLoader.loadClass
  File "ClassLoaders.java", line 178, in jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass
  File "BuiltinClassLoader.java", line 581, in jdk.internal.loader.BuiltinClassLoader.loadClass
java.lang.ClassNotFoundException: java.lang.ClassNotFoundException: org.mastodon.graph.Graph

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 285, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 267, in org.scijava.service.ServiceHelper.createExactService
  File "ServiceHelper.java", line 300, in org.scijava.service.ServiceHelper.createServiceRecursively
  File "Class.java", line 556, in java.lang.Class.newInstance
  File "Class.java", line 3342, in java.lang.Class.getConstructor0
  File "Class.java", line 3137, in java.lang.Class.privateGetDeclaredConstructors
  File "Class.java", line -2, in java.lang.Class.getDeclaredConstructors0
java.lang.NoClassDefFoundError: java.lang.NoClassDefFoundError: org/mastodon/graph/Graph

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 285, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 278, in org.scijava.service.ServiceHelper.createExactService
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\imagej\__init__.py", line 171, in init
    ij = ImageJ()
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Invalid service: org.mastodon.feature.DefaultFeatureComputerService
ctrueden commented 3 years ago

Where is mastodon coming from? That is not part of Fiji. Do you have additional update sites enabled? Could you please try with another copy of Fiji that has no extra update sites enabled?

I also realized you will need to add imglib2-unsafe as well, since it is a dependency of imglib2-imglyb that is not normally part of Fiji.

ghost commented 3 years ago

Oops, my bad. I was testing with my in-use Fiji with a lot of extra update sites enable. Here is the output from the fresh FIJI (from https://imagej.net/software/fiji/) with no additional update sites enabled (as of my current understanding). (I added manually imglib2-unsafe and imglib2-imglyb to JARS folder already).

Thank you.

(base) PS D:\tmp> conda activate pyimagej
(pyimagej) PS D:\tmp> python
Python 3.6.13 (default, Sep 23 2021, 07:38:49) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import logging
>>> logging.basicConfig(level = logging.DEBUG)
>>> import imagej
DEBUG:matplotlib:CONFIGDIR=C:\Users\Z036650\.matplotlib
DEBUG:matplotlib:(private) matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data
DEBUG:matplotlib:matplotlib data path: C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data
DEBUG:matplotlib:loaded rc file C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\matplotlib\mpl-data\matplotlibrc
DEBUG:matplotlib:matplotlib version 3.2.2
DEBUG:matplotlib:interactive is False
DEBUG:matplotlib:platform is win32
DEBUG:matplotlib:loaded modules: ['builtins', 'sys', '_frozen_importlib', '_imp', '_warnings', '_thread', '_weakref', '_frozen_importlib_external', '_io', 'marshal', 'nt', 'winreg', 'zipimport', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', '__main__', 'encodings.latin_1', 'io', 'abc', '_weakrefset', 'site', 'os', 'errno', 'stat', '_stat', 'ntpath', 'genericpath', 'os.path', '_collections_abc', '_sitebuiltins', 'sysconfig', '_bootlocale', '_locale', 'encodings.cp932', '_codecs_jp', '_multibytecodec', 'types', 'functools', '_functools', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'weakref', 'collections.abc', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'mpl_toolkits', 'atexit', 'logging', 'time', 'traceback', 'linecache', 'tokenize', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 'copyreg', 'token', 'string', '_string', 'threading', 'imagej', 'imglyb', 'scyjava', 'jgo', 'jgo.jgo', 'argparse', 'copy', 'textwrap', 'gettext', 'locale', 'struct', '_struct', 'configparser', 'glob', 'fnmatch', 'posixpath', 'pathlib', 'urllib', 'urllib.parse', 'shutil', 'zlib', 'bz2', '_compression', '_bz2', 'lzma', '_lzma', 'subprocess', 'signal', 'msvcrt', '_winapi', 'zipfile', 'binascii', 'hashlib', '_hashlib', '_blake2', '_sha3', 'jgo.util', 'psutil', '__future__', 'datetime', 'math', '_datetime', 'psutil._common', 'socket', '_socket', 'selectors', 'select', 'psutil._compat', 'psutil._pswindows', 'psutil._psutil_windows', 'jpype', '_jpype', 'jpype._jinit', 'jpype._jpackage', 'jpype._jproxy', 'jpype._core', 'jpype.types', 'jpype._jclass', 'jpype._pykeywords', 'jpype._jcustomizer', 'jpype._jobject', 'jpype._jarray', 'jpype._jexception', 'jpype._jstring', 'jpype._classpath', 'jpype._jvmfinder', 'jpype._gui', 'jpype.nio', 'jpype._jmethod', 'jpype._jcollection', 'jpype._jio', 'jpype.protocol', 'decimal', 'numbers', '_decimal', 'typing_extensions', 'typing', 'typing.io', 'typing.re', 'jpype._jthread', 'scyjava.config', 'imglyb.config', 'imglyb.imglib_ndarray', 'ctypes', '_ctypes', 'ctypes._endian', 'numpy', 'numpy._globals', 'numpy.__config__', 'numpy.version', 'numpy._distributor_init', 'numpy.core', 'numpy.core.multiarray', 'numpy.core.overrides', 'numpy.core._multiarray_umath', 'numpy.compat', 'numpy.compat._inspect', 'numpy.compat.py3k', 'pickle', '_compat_pickle', '_pickle', 'numpy.core.umath', 'numpy.core.numerictypes', 'numpy.core._string_helpers', 'numpy.core._type_aliases', 'numpy.core._dtype', 'numpy.core.numeric', 'numpy.core.shape_base', 'numpy.core._asarray', 'numpy.core.fromnumeric', 'numpy.core._methods', 'numpy.core._exceptions', 'numpy.core._ufunc_config', 'numpy.core.arrayprint', 'numpy.core.defchararray', 'numpy.core.records', 'numpy.core.memmap', 'numpy.core.function_base', 'numpy.core.machar', 'numpy.core.getlimits', 'numpy.core.einsumfunc', 'numpy.core._add_newdocs', 'numpy.core._multiarray_tests', 'numpy.core._dtype_ctypes', 'numpy.core._internal', 'ast', '_ast', 'platform', 'numpy._pytesttester', 'numpy.lib', 'numpy.lib.mixins', 'numpy.lib.scimath', 'numpy.lib.type_check', 'numpy.lib.ufunclike', 'numpy.lib.index_tricks', 'numpy.matrixlib', 'numpy.matrixlib.defmatrix', 'numpy.linalg', 'numpy.linalg.linalg', 'numpy.lib.twodim_base', 'numpy.linalg.lapack_lite', 'numpy.linalg._umath_linalg', 'numpy.lib.function_base', 'numpy.lib.histograms', 'numpy.lib.stride_tricks', 'numpy.lib.nanfunctions', 'numpy.lib.shape_base', 'numpy.lib.polynomial', 'numpy.lib.utils', 'numpy.lib.arraysetops', 'numpy.lib.npyio', 'numpy.lib.format', 'numpy.lib._datasource', 'numpy.lib._iotools', 'numpy.lib.financial', 'numpy.lib.arrayterator', 'numpy.lib.arraypad', 'numpy.lib._version', 'numpy.fft', 'numpy.fft._pocketfft', 'numpy.fft._pocketfft_internal', 'numpy.fft.helper', 'numpy.polynomial', 'numpy.polynomial.polynomial', 'numpy.polynomial.polyutils', 'numpy.polynomial._polybase', 'numpy.polynomial.chebyshev', 'numpy.polynomial.legendre', 'numpy.polynomial.hermite', 'numpy.polynomial.hermite_e', 'numpy.polynomial.laguerre', 'numpy.random', 'numpy.random._pickle', 'numpy.random.mtrand', 'cython_runtime', 'numpy.random.bit_generator', '_cython_0_29_24', 'numpy.random._common', 'secrets', 'base64', 'hmac', 'random', 'bisect', '_bisect', '_random', 'numpy.random._bounded_integers', 'numpy.random._mt19937', 'numpy.random._philox', 'numpy.random._pcg64', 'numpy.random._sfc64', 'numpy.random._generator', 'numpy.ctypeslib', 'numpy.ma', 'numpy.ma.core', 'numpy.ma.extras', 'numpy.testing', 'unittest', 'unittest.result', 'unittest.util', 'unittest.case', 'difflib', 'pprint', 'unittest.suite', 'unittest.loader', 'unittest.main', 'unittest.runner', 'unittest.signals', 'numpy.testing._private', 'numpy.testing._private.utils', 'gc', 'tempfile', 'numpy.testing._private.decorators', 'numpy.testing._private.nosetester', 'imglyb.util', 'imglyb.ndarray_like_as_img', 'imglyb.accesses', 'imglyb.caches', 'imglyb.types', 'imglyb.reference_store', 'xarray', 'pkg_resources', 'pkgutil', 'plistlib', 'xml', 'xml.parsers', 'xml.parsers.expat', 'pyexpat.errors', 'pyexpat.model', 'pyexpat', 'xml.parsers.expat.model', 'xml.parsers.expat.errors', 'email', 'email.parser', 'email.feedparser', 'email.errors', 'email._policybase', 'email.header', 'email.quoprimime', 'email.base64mime', 'email.charset', 'email.encoders', 'quopri', 'email.utils', 'email._parseaddr', 'calendar', 'inspect', 'dis', 'opcode', '_opcode', 'pkg_resources.extern', 'pkg_resources._vendor', 'pkg_resources._vendor.six', 'pkg_resources.extern.six', 'pkg_resources._vendor.six.moves', 'pkg_resources.extern.six.moves', 'pkg_resources._vendor.appdirs', 'pkg_resources.extern.appdirs', 'pkg_resources._vendor.packaging', 'pkg_resources._vendor.packaging.__about__', 'pkg_resources.extern.packaging', 'pkg_resources.extern.packaging.version', 'pkg_resources.extern.packaging._structures', 'pkg_resources.extern.packaging._typing', 'pkg_resources.extern.packaging.specifiers', 'pkg_resources.extern.packaging._compat', 'pkg_resources.extern.packaging.utils', 'pkg_resources.extern.packaging.requirements', 'pkg_resources._vendor.pyparsing', 'pkg_resources.extern.pyparsing', 'pkg_resources._vendor.six.moves.urllib', 'pkg_resources.extern.six.moves.urllib', 'pkg_resources.extern.packaging.markers', 'xarray.testing', 'xarray.core', 'xarray.core.duck_array_ops', 'distutils', 'distutils.version', 'pandas', 'pytz', 'pytz.exceptions', 'pytz.lazy', 'pytz.tzinfo', 'pytz.tzfile', 'dateutil', 'dateutil._version', 'pandas.compat', 'pandas.compat.numpy', 'pandas._libs', 'pandas._libs.tslibs', 'pandas._libs.tslibs.conversion', 'pandas._libs.tslibs.c_timestamp', 'pandas._libs.tslibs.nattype', '_cython_0_29_13', 'pandas._libs.tslibs.np_datetime', 'pandas._libs.tslibs.timezones', 'dateutil.tz', 'dateutil.tz.tz', 'six', 'six.moves', 'dateutil.tz._common', 'dateutil.tz._factories', 'dateutil.tz.win', 'ctypes.wintypes', 'pandas._libs.tslibs.tzconversion', 'pandas._libs.tslibs.timedeltas', 'pandas._libs.tslibs.offsets', 'pandas._libs.tslibs.ccalendar', 'pandas._config', 'pandas._config.config', 'pandas._config.dates', 'pandas._config.display', 'pandas._config.localization', 'pandas._libs.tslibs.strptime', 'dateutil.relativedelta', 'dateutil._common', 'pandas._libs.tslibs.fields', 'pandas._libs.tslibs.parsing', 'dateutil.parser', 'dateutil.parser._parser', 'dateutil.parser.isoparser', 'pandas._libs.tslibs.period', 'pandas._libs.tslibs.frequencies', 'pandas._libs.tslibs.timestamps', 'pandas._libs.tslibs.resolution', 'pandas._libs.hashtable', 'pandas._libs.missing', 'pandas._libs.lib', 'fractions', 'pandas._libs.tslib', 'pandas.core', 'pandas.core.config_init', 'pandas.core.api', 'pandas.core.arrays', 'pandas.core.arrays.array_', 'pandas.core.dtypes', 'pandas.core.dtypes.common', 'pandas._libs.algos', 'pandas.core.dtypes.dtypes', 'pandas._libs.interval', 'pandas.core.dtypes.generic', 'pandas.core.dtypes.base', 'pandas.errors', 'pandas.core.dtypes.inference', 'pandas._typing', 'pandas.core.arrays.base', 'pandas.compat.numpy.function', 'pandas.util', 'pandas.util._decorators', 'pandas._libs.properties', 'pandas.core.util', 'pandas.core.util.hashing', 'pandas._libs.hashing', 'pandas.core.dtypes.cast', 'pandas.core.dtypes.missing', 'pandas.util._validators', 'pandas.core.ops', 'pandas._libs.ops', 'pandas.core.common', 'pandas.core.ops.missing', 'pandas.core.ops.roperator', 'pandas.core.ops.docstrings', 'pandas.core.sorting', 'pandas.core.algorithms', 'pandas.core.indexers', 'pandas.core.arrays.categorical', 'pandas.core.accessor', 'pandas.core.base', 'pandas.core.nanops', 'pandas.compat._optional', 'pandas.core.missing', 'pandas.io', 'pandas.io.formats', 'pandas.io.formats.console', 'pandas.core.arrays.datetimes', 'pandas.core.arrays.datetimelike', 'pandas.tseries', 'pandas.tseries.frequencies', 'pandas.tseries.offsets', 'dateutil.easter', 'pandas.core.tools', 'pandas.core.tools.datetimes', 'pandas.core.arrays._ranges', 'pandas.core.arrays.integer', 'pandas.core.tools.numeric', 'pandas.core.arrays.interval', 'pandas.core.indexes', 'pandas.core.indexes.base', 'pandas._libs.index', 'pandas._libs.join', 'pandas.core.dtypes.concat', 'pandas.core.indexes.frozen', 'pandas.io.formats.printing', 'pandas.core.strings', 'pandas.core.arrays.numpy_', 'pandas.core.arrays.period', 'pandas.core.arrays.sparse', 'pandas._libs.sparse', 'pandas.core.arrays.timedeltas', 'pandas.core.groupby', 'pandas.core.groupby.generic', 'pandas.core.frame', 'pandas.core.generic', 'json', 'json.decoder', 'json.scanner', '_json', 'json.encoder', 'pandas.core.index', 'pandas.core.indexes.api', 'pandas.core.indexes.category', 'pandas.core.indexes.datetimes', 'pandas.core.indexes.datetimelike', 'pandas.core.tools.timedeltas', 'pandas.core.indexes.numeric', 'pandas.core.indexes.interval', 'pandas.util._exceptions', 'pandas.core.indexes.multi', 'pandas.core.indexes.timedeltas', 'pandas.core.indexes.period', 'pandas.core.indexes.range', 'pandas.core.indexing', 'pandas._libs.indexing', 'pandas.core.internals', 'pandas.core.internals.blocks', 'pandas._libs.internals', 'pandas.core.internals.arrays', 'pandas.core.internals.managers', 'pandas.core.internals.concat', 'pandas.io.formats.format', 'unicodedata', 'pandas.io.common', 'csv', '_csv', 'gzip', 'http', 'http.client', 'email.message', 'uu', 'email._encoded_words', 'email.iterators', 'ssl', 'ipaddress', '_ssl', 'mmap', 'urllib.error', 'urllib.response', 'urllib.request', 'nturl2path', 'pandas.core.internals.construction', 'pandas.core.series', 'pandas._libs.reshape', 'pandas.core.indexes.accessors', 'pandas.plotting', 'pandas.plotting._core', 'pandas.plotting._matplotlib', 'pandas.plotting._matplotlib.boxplot', 'matplotlib', 'matplotlib.cbook', 'shlex', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.fontconfig_pattern', 'pyparsing', 'pyparsing.util', 'pyparsing.exceptions', 'pyparsing.unicode', 'pyparsing.actions', 'pyparsing.core', 'pyparsing.results', 'pyparsing.helpers', 'html', 'html.entities', 'pyparsing.testing', 'pyparsing.common', 'matplotlib.colors', 'matplotlib.docstring', 'matplotlib._color_data', 'cycler', 'matplotlib._version', 'matplotlib.ft2font', 'kiwisolver']
DEBUG:matplotlib:CACHEDIR=C:\Users\Z036650\.matplotlib
DEBUG:matplotlib.font_manager:Using fontManager instance from C:\Users\Z036650\.matplotlib\fontlist-v310.json
>>> ij = imagej.init("D:\\fiji-win64_vanilla_pyimagej\\Fiji.app")
DEBUG:imagej:Local path to ImageJ installation given: D:\fiji-win64_vanilla_pyimagej\Fiji.app
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ahocorasick-0.2.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/alphanumeric-comparator-1.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/annotations-13.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ant-1.9.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ant-launcher-1.9.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/antlr-3.5.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/antlr-runtime-3.5.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/api-common-1.9.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/args4j-2.0.25.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/asm-7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/asm-analysis-7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/asm-commons-7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/asm-tree-7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/asm-util-7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/auto-value-annotations-1.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/autocomplete-3.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/aws-java-sdk-core-1.11.796.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/aws-java-sdk-kms-1.11.796.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/aws-java-sdk-s3-1.11.796.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/base64-2.3.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batch-processor-0.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-anim-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-awt-util-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-bridge-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-constants-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-css-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-dom-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-ext-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-gvt-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-i18n-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-parser-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-script-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-shared-resources-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-svg-dom-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-svggen-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-util-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/batik-xml-1.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bcpkix-jdk15on-1.62.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bcprov-jdk15on-1.62.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bigdataviewer-core-9.0.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bigdataviewer-vistools-1.0.0-beta-20.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bij-1.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/blas-0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bounce-0.18.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bsh-2.0b6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/bytelist-1.0.15.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/c3p0-0.9.5.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/caffeine-2.4.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/cdm-4.6.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/clojure-1.8.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/codemodel-2.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/collections-generic-4.01.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-beanutils-1.9.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-codec-1.14.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-collections-3.2.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-collections4-4.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-compress-1.20.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-io-2.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-lang-2.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-lang3-3.10.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-logging-1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-math-2.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-math3-3.6.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-text-1.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/commons-vfs2-2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/datasets-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/dirgra-0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ejml-0.24.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/error_prone_annotations-2.3.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/eventbus-1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/f2jutil-0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/failureaccess-1.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/FastInfoset-1.2.16.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ffmpeg-4.1-1.4.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ffmpeg-platform-4.1-1.4.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/fiji-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/fiji-compat-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/fiji-lib-2.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/FilamentDetector-1.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/filters-2.0.235.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gax-1.56.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gax-httpjson-0.73.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gcc-runtime-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gentyref-1.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gluegen-rt-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gluegen-rt-main-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-api-client-1.30.9.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-api-services-cloudresourcemanager-v1-rev20200210-1.30.9.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-api-services-storage-v1-rev20200326-1.30.9.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-auth-library-credentials-0.20.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-auth-library-oauth2-http-0.20.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-cloud-core-1.93.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-cloud-core-http-1.93.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-cloud-resourcemanager-0.117.2-alpha.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-cloud-storage-1.108.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-http-client-1.35.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-http-client-appengine-1.34.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-http-client-jackson2-1.35.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-http-client-xml-1.20.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/google-oauth-client-1.30.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gpars-1.2.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/graphics-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/grDevices-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-dateutil-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-json-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-swing-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-templates-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/groovy-xml-3.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/grpc-context-1.22.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/gson-2.8.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/guava-21.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/httpclient-4.5.12.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/httpcore-4.4.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/httpmime-4.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/httpservices-4.6.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/icu4j-59.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ij-1.53c.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ij1-patcher-1.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/image4j-0.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-2.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-common-0.33.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-deprecated-0.1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-launcher-5.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-legacy-0.37.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-mesh-0.8.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-mesh-io-0.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-notebook-0.7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-ops-0.45.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-plugins-batch-0.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-plugins-commands-0.8.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-plugins-tools-0.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-plugins-uploader-ssh-0.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-plugins-uploader-webdav-0.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-scripting-0.8.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-ui-awt-0.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-ui-swing-0.23.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imagej-updater-0.10.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-5.10.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-algorithm-0.11.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-algorithm-fft-0.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-algorithm-gpl-0.2.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-cache-1.0.0-beta-13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-ij-2.0.0-beta-46.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-imglyb-1.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-label-multisets-0.9.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-realtransform-3.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-roi-0.10.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-ui-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/imglib2-unsafe-0.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/invokebinder-1.10.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ion-java-1.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/istack-commons-runtime-3.0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/itextpdf-5.5.13.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ivy-2.4.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/j2objc-annotations-1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/j3dcore-1.6.0-scijava-2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/j3dutils-1.6.0-scijava-2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackrabbit-webdav-2.21.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackson-annotations-2.11.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackson-core-2.11.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackson-databind-2.11.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackson-dataformat-cbor-2.6.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jackson-jq-1.0.0-preview.20191208.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jai-codec-1.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jai-core-1.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jakarta.activation-api-1.2.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jakarta.xml.bind-api-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jama-1.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/java-cup-11b-20160615.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/java-sizeof-0.0.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/javacpp-1.4.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/javassist-3.27.0-GA.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/javax.annotation-api-1.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/javax.servlet-api-3.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jaxb-runtime-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jblosc-1.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jclipboardhelper-0.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jcodings-1.0.44.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jcommander-1.48.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jcommon-1.0.24.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jdatepicker-1.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jdom2-2.0.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jep-2.4.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jffi-1.2.19-native.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jffi-1.2.20.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jfilechooser-bookmarks-0.1.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jfreechart-1.5.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jfreesvg-3.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jgoodies-common-1.7.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jgoodies-forms-1.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jgrapht-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jgrapht-core-1.4.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jgraphx-4.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jhdf5-14.12.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jheaps-0.11.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jhotdraw-7.6.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jitk-tps-3.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jline-2.14.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jmespath-java-1.11.796.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jna-4.5.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-a64asm-1.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-constants-0.9.12.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-enxio-0.16.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-ffi-2.1.10.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-netdb-1.1.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-posix-3.0.50.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-unixsocket-0.17.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jnr-x86asm-1.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/joal-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/joal-main-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jocl-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jocl-main-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/joda-time-2.10.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jogl-all-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jogl-all-main-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/joml-1.9.25.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/joni-2.1.29.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jpedalSTD-2.80b11.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jply-0.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jruby-core-9.1.17.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jruby-stdlib-9.1.17.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jsch-0.1.55.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/json-20090211.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jsoup-1.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jsr166y-1.7.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jsr305-3.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jtransforms-2.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jung-api-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jung-graph-impl-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/JWlz-1.4.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jython-shaded-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jython-slim-2.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/jzlib-1.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/Kappa-2.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/kotlin-stdlib-1.3.71.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/kotlin-stdlib-common-1.3.71.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/kryo-2.24.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/languagesupport-3.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/lapack-0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/legacy-imglib1-1.1.9.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/log4j-1.2.17.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/logback-classic-1.2.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/logback-core-1.2.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/lz4-java-1.7.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/mapdb-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/markdownj-0.3.0-1.0.2b4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/maven-scm-api-1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/maven-scm-provider-svn-commons-1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/maven-scm-provider-svnexe-1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/mchange-commons-java-0.2.15.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/metadata-extractor-2.11.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/methods-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/miglayout-core-5.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/miglayout-swing-5.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/mines-jtk-20151125.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/minimaven-2.2.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/minio-5.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/minlog-1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/modulator-1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/mpicbg-1.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/mtj-1.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/multiverse-core-0.7.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-2.3.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-aws-s3-3.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-blosc-1.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-google-cloud-3.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-hdf5-1.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-ij-1.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-imglib2-3.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/n5-zarr-0.0.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/nailgun-server-0.9.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/native-lib-loader-2.3.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netcdf-4.3.22.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-buffer-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-codec-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-common-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-handler-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-resolver-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/netty-transport-4.1.45.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/object-inspector-0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/objenesis-2.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ojalgo-45.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/okhttp-4.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/okio-2.6.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/OMEVisual-2.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/op-finder-0.1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/opencensus-api-0.24.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/opencensus-contrib-http-util-0.24.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/opencsv-3.9.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/options-1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/pal-optimization-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/parsington-2.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/perf4j-0.9.16.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/plexus-utils-1.5.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/postgresql-42.2.12.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/prettytime-4.0.1.Final.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/proto-google-common-protos-1.17.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/proto-google-iam-v1-0.13.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/protobuf-java-3.11.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/protobuf-java-util-3.11.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/regexp-1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/renjin-appl-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/renjin-core-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/renjin-gnur-runtime-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/renjin-script-engine-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/rhino-1.7.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/rsyntaxtextarea-3.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scala-compiler-2.12.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scala-library-2.12.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scala-reflect-2.12.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scala-xml_2.12-1.0.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-0.41.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-bf-compat-4.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-cli-0.6.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-hdf5-0.2.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-jai-imageio-1.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-lifesci-0.9.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scifio-ome-xml-0.16.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-common-2.83.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-config-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-io-http-0.2.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-listeners-1.0.0-beta-3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-optional-1.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-plugins-commands-0.2.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-plugins-io-table-0.3.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-plugins-platforms-0.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-plugins-text-markdown-0.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-plugins-text-plain-0.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-search-0.7.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-table-0.6.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-ui-awt-0.1.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scijava-ui-swing-0.13.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/script-editor-0.5.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-beanshell-0.3.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-clojure-0.1.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-groovy-0.3.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-java-0.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-javascript-0.5.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-jruby-0.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-jython-1.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-renjin-0.2.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/scripting-scala-0.2.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/serializer-2.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/slf4j-api-1.7.30.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/snakeyaml-1.26.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/spim_data-2.2.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ST4-4.0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/stats-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/stax-ex-1.8.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/swing-checkbox-tree-1.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/swing-worker-1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/swingx-1.6.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/T2-NIT-1.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/T2-TreelineGraph-1.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/threetenbp-1.4.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/trakem2-transform-1.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/trove4j-3.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/txw2-2.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/udunits-4.3.18.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/ui-behaviour-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/unsafe-fences-1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/utils-0.8.1906.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/vecmath-1.6.0-scijava-2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/VectorGraphics2D-0.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/VectorString-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/VIB-lib-2.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/weave_jy2java-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/weka-dev-3.9.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xalan-2.7.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xchart-3.5.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xerbla-0.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xercesImpl-2.8.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xml-apis-ext-1.3.04.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xmlgraphics-commons-2.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xmpcore-5.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xpp3-1.1.4c.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/xz-1.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars/yecht-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/formats-api-6.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/formats-bsd-6.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/formats-gpl-6.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/jai_imageio-0.0.0-STUB.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/jxrlib-all-0.2.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/metakit-5.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-codecs-0.3.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-common-6.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-jai-0.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-mdbtools-5.3.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-poi-5.3.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/ome-xml-6.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/specification-6.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\bio-formats/turbojpeg-6.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\win64/ffmpeg-4.1-1.4.4-windows-x86_64.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\win64/gluegen-rt-2.3.2-natives-windows-amd64.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\win64/joal-2.3.2-natives-windows-amd64.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\win64/jocl-2.3.2-natives-windows-amd64.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/jars\win64/jogl-all-2.3.2-natives-windows-amd64.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/3D_Blob_Segmentation-3.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/3D_Objects_Counter-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/3D_Viewer-4.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/AnalyzeSkeleton_-3.4.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Anisotropic_Diffusion_2D-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Archipelago_Plugins-0.5.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Arrow_-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Auto_Local_Threshold-1.10.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Auto_Threshold-1.17.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/BalloonSegmentation_-3.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/bigdataviewer_fiji-6.2.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/bigwarp_fiji-6.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/bio-formats_plugins-6.5.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/blockmatching_-2.1.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Bug_Submitter-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/bUnwarpJ_-2.6.13.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Calculator_Plus-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Cell_Counter-3.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Colocalisation_Analysis-3.0.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Color_Histogram-2.0.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Color_Inspector_3D-2.5.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Colour_Deconvolution-3.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/CorrectBleach_-2.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Correct_3D_Drift-1.0.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/CPU_Meter-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Descriptor_based_registration-2.1.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Dichromacy_-2.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Directionality_-2.3.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Feature_Detection-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Fiji_Archipelago-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Fiji_Developer-2.0.7.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Fiji_Package_Maker-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Fiji_Plugins-3.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/FlowJ_-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/FS_Align_TrakEM2-2.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Graph_Cut-1.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Gray_Morphology-2.3.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/H5J_Loader_Plugin-1.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/HDF5_Vibez-1.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Helmholtz_Analysis-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/IJ_Robot-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Image_5D-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Image_Expression_Parser-3.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Interactive_3D_Surface_Plot-3.0.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/IO_-4.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/IsoData_Classifier-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Kuwahara_Filter-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/KymographBuilder-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Lasso_and_Blow_Tool-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/level_sets-1.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Linear_Kuwahara-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/LocalThickness_-4.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/LSM_Reader-4.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/LSM_Toolbox-4.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Manual_Tracking-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/mpicbg_-1.4.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/MTrack2_-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Multi_Kymograph-3.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/M_I_P-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/n5-viewer_fiji-4.0.1-SNAPSHOT.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/panorama_-3.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/PIV_analyser-1.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/QuickPALM_-1.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/RATS_-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Reconstruct_Reader-2.0.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/register_virtual_stack_slices-3.0.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/registration_3d-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Samples_-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Series_Labeler-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Sholl_Analysis-4.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Simple_Neurite_Tracer-3.1.8.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Siox_Segmentation-1.0.5.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Skeletonize3D_-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/SPIM_Opener-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/SPIM_Registration-5.0.21.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/SplineDeformationGenerator_-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Stack_Manipulation-2.1.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Statistical_Region_Merging-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Stitching_-3.1.6.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Sync_Win-1.7-fiji4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Thread_Killer-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Time_Lapse-2.1.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Time_Stamper-2.1.0.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/ToAST_-25.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/TopoJ_-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/TrackMate_-6.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Trainable_Segmentation-3.2.34.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/TrakEM2_-1.3.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/TrakEM2_Archipelago-2.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/trakem2_tps-1.1.4.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Vaa3d_Reader-2.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Vaa3d_Writer-1.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/VIB_-3.0.3.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Video_Editing-2.0.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/View5D_-2.3.1.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Volume_Calculator-2.0.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/Volume_Viewer-2.01.2.jar
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/z_spacing-1.1.1.jar
INFO:imagej:Added 498 JARs to the Java classpath.
DEBUG:scyjava:Adding jars from endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava:Using endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava.config:Getting verbose level: 0
DEBUG:jgo:Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
DEBUG:scyjava:The JVM is already running.
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DEBUG:scyjava:The JVM is already running.
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Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 278, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 267, in org.scijava.service.ServiceHelper.createExactService
  File "ServiceHelper.java", line 315, in org.scijava.service.ServiceHelper.createServiceRecursively
  File "ClassUtils.java", line 163, in org.scijava.util.ClassUtils.getAnnotatedFields
  File "ClassUtils.java", line 193, in org.scijava.util.ClassUtils.getAnnotatedFields
  File "ArrayList.java", line 702, in java.util.ArrayList.addAll
java.lang.NullPointerException: java.lang.NullPointerException

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 278, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 278, in org.scijava.service.ServiceHelper.createExactService
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Z036650\Anaconda3\envs\pyimagej\lib\site-packages\imagej\__init__.py", line 171, in init
    ij = ImageJ()
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Invalid service: sc.fiji.filamentdetector.gui.GUIStatusService
>>>
ghost commented 3 years ago

I'm trying this (renaming filament detector JAR file). I'll update later.

https://forum.image.sc/t/fiji-fails-to-launch-after-update/44582/2

ghost commented 3 years ago

By renaming FilamentDetector JAR file as above URL. I think imagej.init(...) loaded successfully. However

  1. scyjava.get_class() did not work. It seems this method doesn't exist in this version. See below.
  2. When I tried the example of opening an online image file (example from https://github.com/imagej/pyimagej). Errors appeared. Does this look related to proxy setting? How can we tell pyimagej to use some specific proxy setting? (I could access the lena.jpg file normally using my browser). 
    image_url = 'https://samples.fiji.sc/new-lenna.jpg'
jimage = ij.io().open(image_url)

    Opening of offline JPG files are fine. Should I create another issue since pyimagej could initialize successfully now? Can we upate the manual addition of two JARs file and renaming one JAR file above into some documentation?

Thank you.

--- Shortened, same as above ---
------------------------------------------
DEBUG:imagej:Added D:\fiji-win64_vanilla_pyimagej\Fiji.app/plugins/z_spacing-1.1.1.jar
INFO:imagej:Added 497 JARs to the Java classpath.
DEBUG:scyjava:Adding jars from endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava:Using endpoints ['net.imglib2:imglib2-imglyb:1.0.1']
DEBUG:scyjava.config:Getting verbose level: 0
DEBUG:jgo:Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
--- shortened -------------
-----------------------------
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by net.imagej.patcher.LegacyInjector (file:/D:/fiji-win64_vanilla_pyimagej/Fiji.app/jars/ij1-patcher-1.1.0.jar) to method java.lang.ClassLoader.findLoadedClass(java.lang.String)
WARNING: Please consider reporting this to the maintainers of net.imagej.patcher.LegacyInjector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
DEBUG:scyjava:The JVM is already running.
>>> import scyjava
>>> print(scyjava.get_classpath())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'scyjava' has no attribute 'get_classpath'
>>> dir(scyjava)
['ArrayList', 'BigDecimal', 'BigInteger', 'Boolean', 'Byte', 'Character', 'Collection', 'Double', 'Float', 'Integer', 'Iterable', 'Iterator', 'JArray', 'JBoolean', 'JByte', 'JChar', 'JClass', 'JDouble', 'JException', 'JFloat', 'JInt', 'JLong', 'JObject', 'JShort', 'JString', 'JavaCollection', 'JavaIterable', 'JavaIterator', 'JavaList', 'JavaMap', 'JavaObject', 'JavaSet', 'LinkedHashMap', 'LinkedHashSet', 'List', 'Long', 'Map', 'Object', 'Set', 'Short', 'String', 'Void', '_JObject', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '_callbacks', '_import_pandas', '_jstr', '_logger', '_pandas_to_table', '_table_to_pandas', 'collections', 'compare_version', 'config', 'get_version', 'isjava', 'jclass', 'jgo', 'jimport', 'jpype', 'jstacktrace', 'jvm_started', 'logging', 'os', 'scyjava', 'start_jvm', 'to_java', 'to_python', 'when_jvm_starts']
>>> image_url = 'https://samples.fiji.sc/new-lenna.jpg'
>>> jimage = ij.io().open(image_url)
[ERROR] Failed to create handle for location HTTPLocation:https://samples.fiji.sc/new-lenna.jpg
java.net.SocketTimeoutException: connect timed out
        at java.base/java.net.PlainSocketImpl.waitForConnect(Native Method)
        at java.base/java.net.PlainSocketImpl.socketConnect(PlainSocketImpl.java:107)
        at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
        at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
        at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
        at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.base/java.net.Socket.connect(Socket.java:609)
        at okhttp3.internal.platform.Platform.connectSocket(Platform.kt:120)
        at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:283)
        at okhttp3.internal.connection.RealConnection.connect(RealConnection.kt:195)
        at okhttp3.internal.connection.ExchangeFinder.findConnection(ExchangeFinder.kt:249)
        at okhttp3.internal.connection.ExchangeFinder.findHealthyConnection(ExchangeFinder.kt:108)
        at okhttp3.internal.connection.ExchangeFinder.find(ExchangeFinder.kt:76)
        at okhttp3.internal.connection.RealCall.initExchange$okhttp(RealCall.kt:245)
        at okhttp3.internal.connection.ConnectInterceptor.intercept(ConnectInterceptor.kt:32)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.cache.CacheInterceptor.intercept(CacheInterceptor.kt:96)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.BridgeInterceptor.intercept(BridgeInterceptor.kt:83)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.RetryAndFollowUpInterceptor.intercept(RetryAndFollowUpInterceptor.kt:76)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.connection.RealCall.getResponseWithInterceptorChain$okhttp(RealCall.kt:197)
        at okhttp3.internal.connection.RealCall.execute(RealCall.kt:148)
        at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:171)
        at org.scijava.io.http.HTTPHandle.exists(HTTPHandle.java:116)
        at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:386)
        at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:347)
        at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:323)
        at io.scif.services.DefaultDatasetIOService.canOpen(DefaultDatasetIOService.java:87)
        at io.scif.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:70)
        at org.scijava.io.IOService.getOpener(IOService.java:52)
        at org.scijava.io.DefaultIOService.open(DefaultIOService.java:63)
[java.lang.Enum.toString] [ERROR] Failed to create handle for location HTTPLocation:https://samples.fiji.sc/new-lenna.jpg
java.net.SocketTimeoutException: connect timed out
        at java.base/java.net.PlainSocketImpl.waitForConnect(Native Method)
        at java.base/java.net.PlainSocketImpl.socketConnect(PlainSocketImpl.java:107)
        at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
        at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
        at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
        at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.base/java.net.Socket.connect(Socket.java:609)
        at okhttp3.internal.platform.Platform.connectSocket(Platform.kt:120)
        at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:283)
        at okhttp3.internal.connection.RealConnection.connect(RealConnection.kt:195)
        at okhttp3.internal.connection.ExchangeFinder.findConnection(ExchangeFinder.kt:249)
        at okhttp3.internal.connection.ExchangeFinder.findHealthyConnection(ExchangeFinder.kt:108)
        at okhttp3.internal.connection.ExchangeFinder.find(ExchangeFinder.kt:76)
        at okhttp3.internal.connection.RealCall.initExchange$okhttp(RealCall.kt:245)
        at okhttp3.internal.connection.ConnectInterceptor.intercept(ConnectInterceptor.kt:32)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.cache.CacheInterceptor.intercept(CacheInterceptor.kt:96)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.BridgeInterceptor.intercept(BridgeInterceptor.kt:83)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.RetryAndFollowUpInterceptor.intercept(RetryAndFollowUpInterceptor.kt:76)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.connection.RealCall.getResponseWithInterceptorChain$okhttp(RealCall.kt:197)
        at okhttp3.internal.connection.RealCall.execute(RealCall.kt:148)
        at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:171)
        at org.scijava.io.http.HTTPHandle.exists(HTTPHandle.java:116)
        at io.scif.bf.BioFormatsFormat$Checker.isFormat(BioFormatsFormat.java:386)
        at io.scif.services.DefaultFormatService.getFormatList(DefaultFormatService.java:347)
        at io.scif.services.DefaultFormatService.getFormat(DefaultFormatService.java:323)
        at io.scif.services.DefaultDatasetIOService.canOpen(DefaultDatasetIOService.java:87)
        at io.scif.io.DatasetIOPlugin.supportsOpen(DatasetIOPlugin.java:70)
        at org.scijava.io.IOService.getOpener(IOService.java:52)
        at org.scijava.io.DefaultIOService.open(DefaultIOService.java:63)
[INFO] Populating metadata
[java.lang.Enum.toString] [INFO] Populating metadata
[ERROR] Could not create input stream:
java.net.SocketTimeoutException: connect timed out
        at java.base/java.net.PlainSocketImpl.waitForConnect(Native Method)
        at java.base/java.net.PlainSocketImpl.socketConnect(PlainSocketImpl.java:107)
        at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
        at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
        at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
        at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.base/java.net.Socket.connect(Socket.java:609)
        at okhttp3.internal.platform.Platform.connectSocket(Platform.kt:120)
        at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:283)
        at okhttp3.internal.connection.RealConnection.connect(RealConnection.kt:195)
        at okhttp3.internal.connection.ExchangeFinder.findConnection(ExchangeFinder.kt:249)
        at okhttp3.internal.connection.ExchangeFinder.findHealthyConnection(ExchangeFinder.kt:108)
        at okhttp3.internal.connection.ExchangeFinder.find(ExchangeFinder.kt:76)
        at okhttp3.internal.connection.RealCall.initExchange$okhttp(RealCall.kt:245)
        at okhttp3.internal.connection.ConnectInterceptor.intercept(ConnectInterceptor.kt:32)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.cache.CacheInterceptor.intercept(CacheInterceptor.kt:96)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.BridgeInterceptor.intercept(BridgeInterceptor.kt:83)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.RetryAndFollowUpInterceptor.intercept(RetryAndFollowUpInterceptor.kt:76)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.connection.RealCall.getResponseWithInterceptorChain$okhttp(RealCall.kt:197)
        at okhttp3.internal.connection.RealCall.execute(RealCall.kt:148)
        at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:171)
        at org.scijava.io.http.HTTPHandle.in(HTTPHandle.java:85)
        at org.scijava.io.handle.StreamHandle.close(StreamHandle.java:182)
        at org.scijava.io.handle.AbstractHigherOrderHandle.close(AbstractHigherOrderHandle.java:85)
        at io.scif.AbstractReader.setSource(AbstractReader.java:277)
        at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:91)
        at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:80)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:52)
        at org.scijava.io.DefaultIOService.open(DefaultIOService.java:69)
[java.lang.Enum.toString] [ERROR] Could not create input stream:
java.net.SocketTimeoutException: connect timed out
        at java.base/java.net.PlainSocketImpl.waitForConnect(Native Method)
        at java.base/java.net.PlainSocketImpl.socketConnect(PlainSocketImpl.java:107)
        at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
        at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
        at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
        at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.base/java.net.Socket.connect(Socket.java:609)
        at okhttp3.internal.platform.Platform.connectSocket(Platform.kt:120)
        at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:283)
        at okhttp3.internal.connection.RealConnection.connect(RealConnection.kt:195)
        at okhttp3.internal.connection.ExchangeFinder.findConnection(ExchangeFinder.kt:249)
        at okhttp3.internal.connection.ExchangeFinder.findHealthyConnection(ExchangeFinder.kt:108)
        at okhttp3.internal.connection.ExchangeFinder.find(ExchangeFinder.kt:76)
        at okhttp3.internal.connection.RealCall.initExchange$okhttp(RealCall.kt:245)
        at okhttp3.internal.connection.ConnectInterceptor.intercept(ConnectInterceptor.kt:32)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.cache.CacheInterceptor.intercept(CacheInterceptor.kt:96)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.BridgeInterceptor.intercept(BridgeInterceptor.kt:83)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.http.RetryAndFollowUpInterceptor.intercept(RetryAndFollowUpInterceptor.kt:76)
        at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:100)
        at okhttp3.internal.connection.RealCall.getResponseWithInterceptorChain$okhttp(RealCall.kt:197)
        at okhttp3.internal.connection.RealCall.execute(RealCall.kt:148)
        at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:171)
        at org.scijava.io.http.HTTPHandle.in(HTTPHandle.java:85)
        at org.scijava.io.handle.StreamHandle.close(StreamHandle.java:182)
        at org.scijava.io.handle.AbstractHigherOrderHandle.close(AbstractHigherOrderHandle.java:85)
        at io.scif.AbstractReader.setSource(AbstractReader.java:277)
        at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:91)
        at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:80)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:52)
        at org.scijava.io.DefaultIOService.open(DefaultIOService.java:69)
Traceback (most recent call last):
  File "DefaultIOService.java", line 69, in org.scijava.io.DefaultIOService.open
  File "DatasetIOPlugin.java", line 52, in io.scif.io.DatasetIOPlugin.open
  File "DatasetIOPlugin.java", line 80, in io.scif.io.DatasetIOPlugin.open
  File "DefaultDatasetIOService.java", line 133, in io.scif.services.DefaultDatasetIOService.open
  File "DefaultDatasetIOService.java", line 152, in io.scif.services.DefaultDatasetIOService.open
  File "ImgOpener.java", line 242, in io.scif.img.ImgOpener.openImgs
  File "ImgOpener.java", line 483, in io.scif.img.ImgOpener.createReader
  File "DefaultInitializeService.java", line 91, in io.scif.services.DefaultInitializeService.initializeReader
  File "AbstractReader.java", line 271, in io.scif.AbstractReader.setSource
  File "AbstractParser.java", line 53, in io.scif.AbstractParser.parse
  File "AbstractParser.java", line 314, in io.scif.AbstractParser.parse
  File "AbstractParser.java", line 244, in io.scif.AbstractParser.parse
  File "JPEGFormat.java", line 146, in io.scif.formats.JPEGFormat$Parser.typedParse
  File "JPEGFormat.java", line 158, in io.scif.formats.JPEGFormat$Parser.typedParse
  File "ImageIOFormat.java", line 135, in io.scif.formats.ImageIOFormat$Parser.typedParse
io.scif.FormatException: io.scif.FormatException: Invalid image stream

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "DefaultIOService.java", line 69, in org.scijava.io.DefaultIOService.open
  File "DatasetIOPlugin.java", line 52, in io.scif.io.DatasetIOPlugin.open
  File "DatasetIOPlugin.java", line 80, in io.scif.io.DatasetIOPlugin.open
  File "DefaultDatasetIOService.java", line 133, in io.scif.services.DefaultDatasetIOService.open
  File "DefaultDatasetIOService.java", line 152, in io.scif.services.DefaultDatasetIOService.open
  File "ImgOpener.java", line 242, in io.scif.img.ImgOpener.openImgs
  File "ImgOpener.java", line 483, in io.scif.img.ImgOpener.createReader
  File "DefaultInitializeService.java", line 91, in io.scif.services.DefaultInitializeService.initializeReader
  File "AbstractReader.java", line 279, in io.scif.AbstractReader.setSource
java.io.IOException: java.io.IOException: io.scif.FormatException: Invalid image stream

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "DefaultIOService.java", line 69, in org.scijava.io.DefaultIOService.open
  File "DatasetIOPlugin.java", line 52, in io.scif.io.DatasetIOPlugin.open
  File "DatasetIOPlugin.java", line 80, in io.scif.io.DatasetIOPlugin.open
  File "DefaultDatasetIOService.java", line 133, in io.scif.services.DefaultDatasetIOService.open
  File "DefaultDatasetIOService.java", line 152, in io.scif.services.DefaultDatasetIOService.open
  File "ImgOpener.java", line 242, in io.scif.img.ImgOpener.openImgs
  File "ImgOpener.java", line 489, in io.scif.img.ImgOpener.createReader
io.scif.img.ImgIOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid image stream

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "DefaultIOService.java", line 69, in org.scijava.io.DefaultIOService.open
  File "DatasetIOPlugin.java", line 52, in io.scif.io.DatasetIOPlugin.open
  File "DatasetIOPlugin.java", line 80, in io.scif.io.DatasetIOPlugin.open
  File "DefaultDatasetIOService.java", line 133, in io.scif.services.DefaultDatasetIOService.open
  File "DefaultDatasetIOService.java", line 163, in io.scif.services.DefaultDatasetIOService.open
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
java.io.IOException: java.io.IOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid image stream
>>>
hinerm commented 3 years ago

@phamtronglam

scyjava.get_class() did not work. It seems this method doesn't exist in this version. See below.

The method is get_classpath() and it's in scyjava.config, not scyjava base. e.g.:

import scyjava.config as sjc
print(sjc.get_classpath())

When I tried the example of opening an online image file (example from https://github.com/imagej/pyimagej). Errors appeared. Does this look related to proxy setting?

Yes it does look like it's also related to being behind your firewall :(

Can we upate the manual addition of two JARs file and renaming one JAR file above into some documentation?

I added this section to the troubleshooting guide.

The renaming FilamentDetector is bizarre and I'm surprised it came up. Does your Fiji have a FilamentDetector 1.x jar? In an up-to-date Fiji it should be 2.0.0 which I believe @ctrueden fixed (1.x required JavaFX which isn't present in the conda-distributed Java runtime)

ghost commented 3 years ago

@hinerm Thank you very much.

  1. sjc.get_classpath() works now.

  2. Is there a way to tell jimage = ij.io().open(image_url) to use some proxy settings? I already setup ~/.m2/settings.xml but it doesnot seem to affect this command.

    Yes it does look like it's also related to being behind your firewall :(

  3. Thank you very much about

    I added this section to the troubleshooting guide.

  4. Unfortunately I could not find FilamentDetector-2.0.0.jar anywhere. (Latest fiji download; latest FIJI update sites; and FilamentDetector github site https://sites.imagej.net/FilamentDetector/jars/ all pointed to the latest being FilamentDetector-1.0.0.jar :(

    The renaming FilamentDetector is bizarre and I'm surprised it came up. Does your Fiji have a FilamentDetector 1.x jar? In an up-to-date Fiji it should be 2.0.0 which I believe @ctrueden fixed (1.x required JavaFX which isn't present in the conda-distributed Java runtime)

ctrueden commented 3 years ago

Unfortunately I could not find FilamentDetector-2.0.0.jar anywhere.

Please disable the FilamentDetector update site; it is obsolete. FilamentDetector is now shipped on the core update site: https://sites.imagej.net/Java-8/jars/

Is there a way to tell jimage = ij.io().open(image_url) to use some proxy settings?

Try this:

System = scyjava.jimport('java.lang.System')
System.setProperty("http.proxyHost","myproxy.domain")
System.setProperty("http.proxyPort","8080")

Where myproxy.domain and 8080 are your domain and port, respectively.

ghost commented 3 years ago

@ctrueden Thank you very much. Problem solved now!!

I manually downloaded FilamentDetector-2.0.0.jar from https://sites.imagej.net/Java-8/jars/ and it doesnot complain about FilamentDetector anymore.

Thank you very much for the proxy settings. I had to use https.proxyHost and https.proxyPort also. I think this could be relected into Troubleshooting to make life easier for people behind firewall like me.

Thank you very much!!

hinerm commented 3 years ago

I think this could be relected into Troubleshooting to make life easier for people behind firewall like me.

Resolved in https://github.com/imagej/pyimagej/commit/7bfb9f80d420122bb0fbb8d4d8ce7d5a2a09eb7d

jan-glx commented 2 years ago

JAVA_TOOL_OPTIONS+=" -Djava.net.useSystemProxies=true" python3 -c 'import imagej; ij = imagej.init("2.1.0"); print(ij.getVersion()); ij.dispose()' did the trick for me

ctrueden commented 2 years ago

@jan-glx Hey, thanks! I didn't know about (or forgot) -Djava.net.useSystemProxies=true. That's great to know.

ctrueden commented 2 years ago

@jan-glx OK, I finally got around to trying out your suggestion, because I want to add it to the doc/Troubleshooting.md and/or do it automatically in the code.

But I'm wondering, which piece of the architecture picks up the JAVA_FLAGS environment variable? I can't find a reference to it anywhere, not in JPype, nor scyjava, nor pyimagej, nor jgo, nor Maven. And in all my tests, flags I pass by setting them in that way do not propagate into the Java runtime. Are you sure it works that way? For example, does the following script print bar for you?

JAVA_FLAGS=-Dfoo=bar python3 -c 'import scyjava; System = scyjava.jimport("java.lang.System"); print(System.getProperty("foo"))'

There is a variable MAVEN_OPTS for this purpose for Maven, which could help with mvn downloading dependencies: see the docs here.

jan-glx commented 2 years ago

Sorry, the JAVA_FLAGS indeed doesn't seem to be picked up! ( I think I used System.setProperty to set it and did not test the JAVA_FLAGS way, main point was to to set java.net.useSystemProxies=true instead of the manual configuation)

There is a way that keeps a users source code clean though (JAVA_TOOL_OPTIONS):

JAVA_TOOL_OPTIONS+=" -Djava.net.useSystemProxies=true" python3 -c 'import scyjava; System = scyjava.jimport("java.lang.System"); print(System.getProperty("java.net.useSystemProxies"))'
# Picked up JAVA_TOOL_OPTIONS:  -Djava.net.useSystemProxies=true
# true

(will edit above post accordingly)

ctrueden commented 2 years ago

Thanks @jan-glx, I have now improved the Troubleshooting document to recommend JAVA_TOOL_OPTIONS!